Sorry, I do not know why the "%22" is being inserted into the URL however I can offer this as a workaround.
Use a VBScript to run IE passing it the URL as a argument.
I created the attached startie.vbs script in C:\Windows and used the following command to start IE opening to Google.
"/Applications/VMware Fusion.app/Contents/Library/vmrun" -T fusion -gu <user> -gp <pass> runScriptInGuest "<path to .vmx file>" -noWait -interactive "" "cscript.exe \"C:\\Windows\\startie.vbs\" http://www.google.com"
The script is just a few lines and for some reason I had to set the FQP of iexplore.exe to its 8.3 equivalent however the script works and is only meant as a workaround as I do not have the time to investigate why you're getting the results your are.
startie.vbs script:
Dim strIE
Dim objArgs
strIE = "C:\Progra~1\Intern~1\iexplore.exe"
Set objArgs = Wscript.Arguments
Set WshShell = WScript.CreateObject("WScript.Shell")
WshShell.Run strIE & " " & objArgs(0)